They're given limited resources and are asked to write software to a certain spec. And in order to make that software as good as possible within the given limitations, they resort to all kinds of interesting solutions. Quite often it's things they haven't tried before, ideas they get as they go. Yes, it's very seldom a world premiere for those ideas. But within the realm of experience of a particular programmer, he innovates.

Obviously if Microsoft or Apple recreated apt-get and made it work for windows/osx down to the last command line option, then you would be admiring them for the great "Innovation" ......

The GNU project is many things, but not innovative by any stretch of the imagination.